The present invention relates generally to the field of biochemistry, and more particularly to determining the optimal biosensing surface area to reduce false detection of nucleotides.
Surface hybridization, in which an immobilized probe single-stranded DNA (ss-DNA) of known sequence recognizes the complementary target ss-DNA (c-DNA) molecule, is central to DNA biosensing technologies and novel nanodevices. These techniques are being extensively applied in a number of important fields such as genotyping, gene expression profiling, and biological detection. Hybridization at the solid/liquid interface can be significantly promoted by nonspecific adsorption of the target ss-DNA and the consequent two-dimensional search. Several other factors such as probe density, probe and linker length, surface topology, and surface chemistry further affect surface hybridization, thus making hybridization on surface more complicated than that in solution. However, if would be advantageous to design an optimal surface hybridization protocol.
Gold has been extensively used to study the interactions governing surface hybridization due to its many useful properties as a model substrate. However, hybridization on gold is affected by nonspecific adsorption of the exposed bases of small strand DNA or ss-DNA. Nonspecific DNA gold interaction is found to be base-dependent, following the order A>G>C>T. Typical probe sequences (nucleotides) at low surface densities exhibit hybridization efficiency of greater than 60% that is lower than what is observed in solution. A planar gold surface has been reported to significantly slow down and lower free energy of hybridization. Studies also suggested incomplete hybridization on gold. Due to typical probe sequences non-specific interactions with gold, the use of gold, as presented in more detail below, in order to increase the sensitivity and accuracy of probe-gold interactions is not an obvious solution.